Determination of intersubunit distances and subunit shape parameters in DNA-dependent RNA polymerase by neutron small-angle scattering

In all organisms the multi-subunit enzyme DNA-dependent RNA polymerase catalyses the first basic step in gene expression, the transcription of DNA into RNA. The neutron small-angle scattering effects were studied in the Guinier region by applying the contrast-matching technique. Isotopic labelling was realised by culturing fully deuterated E. coli cells in a heavy-water medium containing deuterated substrates. One or two completely deuterated components (subunits) of polymerase holoenzyme (composition formula α₂ββ′σ, molecular weight 497000) were recombined with the remaining natural (`hydrogenated') subunits for these neutron measurements. Measurements are presented of radii of gyration R, overall shapes, and pair distances d, of three components (subunits α₂β,β′) in RNA polymerase of E. coli. The subunits β′, β and α₂ are obviously rather elongated in situ and exhibit (as scattering-equivalent prolate ellipsoids) axial ratios of about 7:1 up to 9:1. The intersubunit centre of gravity distances were analysed to be 7.3 ± 0.8 nm for β−β′, 8.2 ± 1.2 nm for α₂−β′ and 7.0 ± 1.7 nm for α₂−β.